Just a guess, if the amp sounds fine still and the tubes look good -- not "cherried", the trouble lights could have been on the whole time since you got it back. I suspect that the trouble indicators could have something to do with varying from the factory bias spec. The tubes might be biased hotter or colder than some magic Fender-specified range. This is done to fine tune for tone or power output or tube life, etc. (not at the same time, of course!) I'd call the tech who put in the new tubes and tell him your problem.
I couldn't get a hold of the factory manual but here's a dibby-dab from the Fender site about your model:
The TROUBLE LED’s and BIAS POTS let the user diagnose failed output tubes, install new tubes, and set the optimum bias without the aid of a technician. This saves the customer time and money.
Good luck!